Cao Yang,
About DPPC see
http://pubs.acs.org/doi/abs/10.1021/jp212503e
The authors have used R.E.D.
regards, Francois
Quoting FyD <fyd.q4md-forcefieldtools.org>:
> Dear Cao Yang,
>
>> I am a user of AMBER in China. My system is a protein complex with
>> phospholipid membranes. The particial charge of DPPC is calculated
>> in GAUSSIAN.
>
> MEP are computed using a QM program and charges are usually derived
> from the MEP during an additional fitting step (using for instance the
> RESP program). Indeed, even if the QM program provides with the MEP a
> set of charge values (ESP) they are generally not suitable for MD
> simulations as they are not equivalenced (chemical equivalencing for
> chemical equivalent atoms lead to identical charge values for atoms
> that are chemically equivalent: this is achieved during the fitting
> stage(s) by using specific charge constraints).
>
>> The charge of my ligand is calculated in AMBER with AM1.
>> I load the pdb file into tleap and find the whole charge of my
>> system is +5.6. So I add 6 Cl- which change the charge to -0.4
>> rather than zero. I wonder why the total charge is not zero. So My
>> question is:
>>
>> Whether the charge equaling -0.4 be resonable in MD simulation? If
>> not, how should I make the system neutral?
>> Thanks for your time!
>
> - The total charge of a whole molecule such as DPPC should be an
> integer value.
> - If you generated a molecular fragment from the DPPC molecule one
> could imagine a non-integer charge value for a molecular fragment, but
> in this case the sum of the total charges of the different molecular
> fragments constructed should lead to an integer charge value.
>
> You can find two examples of lipids in R.E.DD.B. This corresponds to
> the work of S. Abel. See:
> http://q4md-forcefieldtools.org/REDDB/projects/F-72/
> http://q4md-forcefieldtools.org/REDDB/projects/F-92/
>
> In F-92, dodecylphosphocholine (DPC) is constructed from 3 elementary
> building blocks... This is quite simple to adapt this approach to the
> DPPC case.
>
> You might also look for in the literature for already available parameters...
>
> regards, Francois
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Received on Sun Apr 29 2012 - 04:00:03 PDT
